Xarray_Map_Plotting_Workflow

ecology-x-array-map-plot/main-workflow

Author(s)
Soumya Jha
Version
1
Last updated
Oct 26, 2022
License
MIT
Tags
ecology
climate

Features
Tutorial
Visualization of Climate Data using NetCDF xarray Map Plotting
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00062
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nair_temperature_at_2_metres.nc"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["NetCDF xarray Coordinate Info"];
  0 -->|output| 1;
  2["NetCDF xarray Metadata Info"];
  0 -->|output| 2;
  3["CDO Operations"];
  0 -->|output| 3;
  4["CDO Operations"];
  3 -->|output_files| 4;
  5["NetCDF xarray Metadata Info"];
  4 -->|output_files| 5;
  6["NetCDF xarray map plotting"];
  4 -->|output_files| 6;
  5 -->|output| 6;
  7["NetCDF xarray map plotting"];
  4 -->|output_files| 7;
  5 -->|output| 7;

Inputs

Input Label
Input dataset air_temperature_at_2_metres.nc

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0 NetCDF xarray Coordinate Info
toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1 NetCDF xarray Metadata Info
toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0 CDO Operations
toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0 CDO Operations
toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1 NetCDF xarray Metadata Info
toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0 NetCDF xarray map plotting
toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0 NetCDF xarray map plotting

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/climate/cdo_operations/cdo_operations/2.0.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/xarray_coords_info/xarray_coords_info/0.20.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/xarray_mapplot/xarray_mapplot/0.20.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 ce9cd3e8d 2022-10-26 18:20:31 Tutorial added to ecology folder: "Visualization of Climate Data using NetCDF Xarray Map Plotting" (#3481)

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/ecology/tutorials/x-array-map-plot/workflows/main-workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows